VMD-L Mailing List

From: Kramer Campen (campen_at_geosc.psu.edu)
Date: Thu May 17 2007 - 17:45:28 CDT

See below...

kramer

At 05:44 PM 5/17/2007 -0400, Mark Zottola wrote:
>I am new to VMD and would like to be able to do some things which do not
>(apparently) exist in the manual.
>
All of these exist in the manual but are perhaps not so easy to find if you
don't know what you're looking for.

>1) I would like to be able to take and generate pdb files from a select
>number of frames from and MD simulation.

You can easily do this by hand (if you only have a few frames) by simply
choosing "save coordinates" (see
http://www.ks.uiuc.edu/Research/vmd/current/ug/node35.html#SECTION00742200000000000000
in the manual for more discussion).

>
>2) I would like to be able to monitor the number of water molecules near
>an active site residue over the course of a simulation as well as
>calculate distances of these waters from a particular atom in the active
>site..

You can do this a number of different ways most of which involve using the
"measure" command (see
http://www.ks.uiuc.edu/Research/vmd/current/ug/node124.html in the manual
for more discussion).

>
>3) I would like to monitor the distance between two atoms in 2 different
>residues over the course of a simulation.

You can easily do this by hand by first changing the mouse pick mode to
"label distance" (see
http://www.ks.uiuc.edu/Research/vmd/current/ug/node38.html#SECTION00745100000000000000
in the manual for discussion) and then moving to the labels form (see
http://www.ks.uiuc.edu/Research/vmd/current/ug/node41.html in the manual
for further explanation) from where you easily save or graph the results.

>
>Are these best done by writing a Tcl script? Are there built in functions
>to do this?

If you have to do a lot of any of this its probably worth it to script the
commands but otherwise...

>
>Thanks for any help you can send my way!
>
>
>Mark
>